• Proceedings of the Earthquake Engineering Society of Korea Conference
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• 2001.09a
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• pp.67-74
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• 2001

This paper presents the Safe Shutdown Earthquake(SSE) input motion for the seismic design of the Advanced Power Reactor 1400(APR1400). The Design Ground Response Spectra(DGRS) far the SSE is based on the design spectrum specified in regulatory Guide(RG) 1.60 of U.S. Nuclear Regulatory Commission(US NRC), anchored to a Peak Ground Acceleration(PGA) of 0.3g and enriched in the high frequency range. This SSE seismic input motion is to be applied to the seismic analysis as the free-field seismic motion at the ground surface of both the rock and generic soil sites fur APRI1400. The enrichment for APR1400 seismic input motion is performed considering the current US NRC regulations, the seismic hazard studies performed by the Lawrence Livermore National Laboratory (LINL) and Electric Power Research Institute(EPRI) for the Central and Eastern United States nuclear power plant sites, and the seismic input motions used in the design certifications of the three existing U.S. advanced standard plants. It is represented by a set of DGRS and the accompanying Target Power Spectral Density(PSD) Function in both the horizontal and vertical directions.

• 한국균학회소식:학술대회논문집
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• 2016.05a
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• pp.17-17
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• 2016

Calcineurin governs stress survival, sexual differentiation, and virulence of the human fungal pathogen Cryptococcus neoformans. Herein, we identified and characterized calcineurin substrates in C. neoformans by employing phosphoproteomic $TiO_2$ enrichment and quantitative mass spectrometry. The identified targets include the zinc finger transcription factor Crz1 and proteins whose functions are linked to P-bodies/stress granules (PBs/SGs) and mRNA translation and decay, such as Pbp1 and Puf4. We show that Crz1 is a bona fide calcineurin substrate, and localization and transcriptional activity of Crz1 are controlled by calcineurin. Several of the calcineurin targets localized to PBs/SGs, including Puf4 and Pbp1, and are required for survival at high temperature and for virulence. Genetic epistasis analysis revealed that Crz1 and the novel targets Lhp1, Puf4, and Pbp1 function in a branched calcineurin pathway that orchestrates stress survival and virulence. These findings propose that calcineurin controls thermal stress and virulence at the transcriptional level via Crz1 and post-transcriptionally by regulating target factors involved in mRNA metabolism.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.8
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• pp.4553-4557
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• 2013

Objective: The purpose of this study was to identify genes related to bladder cancer with samples from normal and disease cases by microarray chip. Methods: After downloading the gene expression profile GSE3167 from Gene Expression Omnibus database which includes 50 bladder samples, comprising 9 normal and 41 disease samples, differentially expressed genes were identified with packages in R language. The selected differentially expressed genes were further analyzed using bioinformatics methods. Firstly, molecular functions, biological processes and cell component analysis were researched by software Gestalt. Then, software String was used to search interaction relationships among differentially expressed genes, and hub genes of the network were selected. Finally, by using plugins of software Cytoscape, Mcode and Bingo, module analysis of hub-genes was performed. Results: A total of 221 genes were identified as differentially expressed by comparing normal and disease bladder samples, and a network as well as the hub gene C1QBP was obtained from the network. The C1QBP module had the closest relationship to production of molecular mediators involved in inflammatory responses. Conclusion: We obtained differentially expressed genes of bladder cancer by microarray, and both PRDX2 and YWHAZ in the module with hub gene C1QBP were most significantly related to production of molecular mediators involved in inflammatory responses. From knowledge of inflammatory responses and cancer, our results showed that, the hub gene and its module could induce inflammation in bladder cancer. These related genes are candidate bio-markers for bladder cancer diagnosis and might be helpful in designing novel therapies.

• Fisheries and Aquatic Sciences
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• v.26 no.9
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• pp.569-581
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• 2023

The morphology and genetic identification of Rasbora lateristriata and Rasbora argyrotaenia between cultivated and wild populations has never been reported. This study compares morphology and cytochrome c oxidase (COI) genes between farmed and wild stock Rasbora spp. in Java and Sumatra island, Indonesia. We analyzed the truss network measurement (TNM) characters of 80 fish using discriminant function analysis statistical tests. DNA was extracted from muscle tissue of 24 fish specimens, which was then followed by polymerase chain reaction, sequencing, phylogenetic analysis, fixation index analysis, and statistical analysis of haplotype networks. Basic Local Alignment Search Tool analysis validated the following species: R. lateristriata and R. argyrotaenia from farming (Jogjakarta); Rasbora agryotaenia (Purworejo), R. lateristriata (Purworejo and Malang), Rasbora dusonensis (Palembang), and Rasbora einthovenii (Riau) from natural resources. Based on TNM characters, Rasbora spp. were divided into four groups, referring to four distinct characters in the middle of the body. The phylogenetic tree is divided into five clades. The genetic distance between R. argyrotaenia (Jogjakarta) and R. lateristriata (Malang) populations (0.66) was significantly different (p < 0.05). R. lateristriata (Purworejo) has the highest nucleotide diversity (0.43). R. argyrotaenia from Jogjakarta and Purworejo shared the same haplotype. The pattern of gene flow among them results from the two populations' close geographic proximity and environmental effects. R. argyrotaenia had low genetic diversity, therefore, increasing heterozygosity in cultivated populations is necessary to avoid inbreeding. Otherwise, R. lateristriata (Purworejo) had a greater gene variety that could be used to develop breeding. In conclusion, the middle body parts are a distinguishing morphometric character of Rasbora spp., and the COI gene is more heterozygous in the wild population than in farmed fish, therefore, enrichment of genetic variation is required for sustainable Rasbora fish farming.

• Journal of Life Science
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• v.19 no.8
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• pp.1159-1163
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• 2009

It has been postulated that endoplasmic (ER) stress is involved in the development of several diseases. However, the detailed molecular mechanisms have not been fully understood. Therefore, we characterized a genetic network of genes induced by ER stress using cDNA microarray and gene set expression coherence analysis (GSECA), and identified gene function as well as several transcription regulators associated with ER stress. We analyzed time-dependent gene expression profiles in thapsigargin-treated Sk-Hep1 using an oligonucleotide expression chip, and then selected functional gene sets with significantly high expression coherence which was processed into functional clusters according to the expression similarities. The functions related to sugar binding, lysosome, ribosomal protein, ER lumen, and ER to golgi transport increased, whereas the functions with mRNA processing, DNA replication, DNA repair, cell cycle, electron transport chain and helicase activity decreased. Furthermore, functional clusters were investigated for the enrichment of regulatory motifs using GSECA, and several transcriptional regulators associated with regulation of ER-induced gene expression were found.

• Steel and Composite Structures
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• v.37 no.6
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• pp.663-678
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• 2020

This paper proposes a novel topology optimization method generating multiple materials for external linear plane crack structures based on the combination of IsoGeometric Analysis (IGA) and eXtended Finite Element Method (X-FEM). A so-called eXtended IsoGeometric Analysis (X-IGA) is derived for a mechanical description of a strong discontinuity state's continuous boundaries through the inherited special properties of X-FEM. In X-IGA, control points and patches play the same role with nodes and sub-domains in the finite element method. While being similar to X-FEM, enrichment functions are added to finite element approximation without any mesh generation. The geometry of structures based on basic functions of Non-Uniform Rational B-Splines (NURBS) provides accurate and reliable results. Moreover, the basis function to define the geometry becomes a systematic p-refinement to control the field approximation order without altering the geometry or its parameterization. The accuracy of analytical solutions of X-IGA for the crack problem, which is superior to a conventional X-FEM, guarantees the reliability of the optimal multi-material retrofitting against external cracks through using topology optimization. Topology optimization is applied to the minimal compliance design of two-dimensional plane linear cracked structures retrofitted by multiple distinct materials to prevent the propagation of the present crack pattern. The alternating active-phase algorithm with optimality criteria-based algorithms is employed to update design variables of element densities. Numerical results under different lengths, positions, and angles of given cracks verify the proposed method's efficiency and feasibility in using X-IGA compared to a conventional X-FEM.

• Journal of Nuclear Fuel Cycle and Waste Technology(JNFCWT)
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• v.9 no.3
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• pp.191-198
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• 2011

In general, conventional criticality analyses for spent fuel transport/dry storage systems have been performed based on assumption of fresh fuel concerning the potential uncertainties from number density calculation of Transuranic and Fission Products in spent fuel. However, because of economic loss due to the excessive criticality margin, recently the design of transport/dry storage systems with Burnup Credit(BUC) application has been actively developed. The uncertainties in criticality analyses on transport/storage systems with BUC technique show strong dependance upon initial enrichment and burnup rate, whereas those in the conventional criticality evaluation based on fresh fuel assumption do not show such a dependance. In this study, regulatory-required uncertainties of the criticality analyses for BK 26 Cask, which is conceptually designed spent fuel transport cask with BUC corresponding to the limiting circumstances on nuclear power plants in Korea, are evaluated as a function of initial enrichment and burnup rate. Results of this study will be used as basic data for spent fuel loading curve of BK 26 Cask.

• Korean Journal of Construction Engineering and Management
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• v.17 no.2
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• pp.90-98
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• 2016

High-rise buildings construction project have various risk factors. Major risk factors are negative results such as time delay and increase of costs. Therefore, this study was analyzed risk factors in construction stages of high-rise buildings using by PROMETHEE technique. For this, this research were identified risk factors through experts Focus Group Interview(FGI). And, PROMETHEE was used to setup evaluation standard for analysis of high-rise building construction risks. Next, the standard of evaluation index calculation was composed by using the definition level in PDRI. Preference function and evaluation index were identified through questionnaires. Through these processes, this study has calculated the importance of high-rise building construction risks using by PROMETHEE technique. As a result, high degree risk factors were as following. These are 'Operation plan of material lifting', 'Outrigger & Belt Truss Construction', 'Foundation work plan of high-rise building' and 'Considering a Structure concept of high-rise building'.

• Genomics & Informatics
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• v.5 no.1
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• pp.10-18
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• 2007

Numerous studies have reported that genes with similar expression patterns are co-regulated. From gene expression data, we have assumed that genes having similar expression pattern would share similar transcription factor binding sites (TFBSs). These function as the binding regions for transcription factors (TFs) and thereby regulate gene expression. In this context, various analysis tools have been developed. However, they have shortcomings in the combined analysis of expression patterns and significant TFBSs and in the functional analysis of target genes of significantly overrepresented putative regulators. In this study, we present a web-based A Functional Clustering Analysis Tool for Predicted Transcription Regulatory Elements and Gene Ontology Terms (FCAnalyzer). This system integrates microarray clustering data with similar expression patterns, and TFBS data in each cluster. FCAnalyzer is designed to perform two independent clustering procedures. The first process clusters gene expression profiles using the K-means clustering method, and the second process clusters predicted TFBSs in the upstream region of previously clustered genes using the hierarchical biclustering method for simultaneous grouping of genes and samples. This system offers retrieved information for predicted TFBSs in each cluster using $Match^{TM}$ in the TRANSFAC database. We used gene ontology term analysis for functional annotation of genes in the same cluster. We also provide the user with a combinatorial TFBS analysis of TFBS pairs. The enrichment of TFBS analysis and GO term analysis is statistically by the calculation of P values based on Fisher’s exact test, hypergeometric distribution and Bonferroni correction. FCAnalyzer is a web-based, user-friendly functional clustering analysis system that facilitates the transcriptional regulatory analysis of co-expressed genes. This system presents the analyses of clustered genes, significant TFBSs, significantly enriched TFBS combinations, their target genes and TFBS-TF pairs.

• Genomics & Informatics
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• v.21 no.2
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• pp.22.1-22.15
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• 2023

Kidney renal clear cell carcinoma (KIRC) is one of the most aggressive cancer type of the urinary system. Metastatic KIRC patients have poor prognosis and limited therapeutic options. Ankyrin 3 (ANK3) is a scaffold protein that plays important roles in maintaining physiological function of the kidney and its alteration is implicated in many cancers. In this study, we investigated differential expression of ANK3 in KIRC using GEPIA2, UALCAN, and HPA databases. Survival analysis was performed by GEPIA2, Kaplan-Meier plotter, and OS-kirc databases. Genetic alterations of ANK3 in KIRC were assessed using cBioPortal database. Interaction network and functional enrichment analyses of ANK3-correlated genes in KIRC were performed using GeneMANIA and Shiny GO, respectively. Finally, the TIMER2.0 database was used to assess correlation between ANK3 expression and immune infiltration in KIRC. We found that ANK3 expression was significantly decreased in KIRC compared to normal tissues. The KIRC patients with low ANK3 expression had poorer survival outcomes than those with high ANK3 expression. ANK3 mutations were found in 2.4% of KIRC patients and were frequently co-mutated with several genes with a prognostic significance. ANK3-correlated genes were significantly enriched in various biological processes, mainly involved in peroxisome proliferator-activated receptor (PPAR) signaling pathway, in which positive correlations of ANK3 with PPARA and PPARG expressions were confirmed. Expression of ANK3 in KIRC was significantly correlated with infiltration level of B cell, CD8+ T cell, macrophage, and neutrophil. These findings suggested that ANK3 could serve as a prognostic biomarker and promising therapeutic target for KIRC.